Re: [Gmod-gbrowse] GBrpwse2.0 error

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Re: [Gmod-gbrowse] GBrpwse2.0 error

Scott Cain
Hi Sal,

I'm cc'ing the JBrowse mailing list so this conversation can be archived and others can chime in to help.  

When you say you followed all the tutorials, what does that mean exactly?  Did you run prepare-refseqs.pl and flatfile-to-json.pl? There is a reasonably good tutorial that I present in a few different settings, like this one that I gave at the Plant and Animal Genomes meeting in January: 


You wouldn't need the 3 GB virtualbox image linked at the top of the page, but you could use the commented out "curl" command in the "Setting up JBrowse" section to get the files used for the tutorial.

Scott


On Thu, Jul 27, 2017 at 5:47 PM, Salvatore Esposito <[hidden email]> wrote:
Hi Scott
how are you?
First, I wanna say you thanks again to suggest me jbrowse. I installed it and follow all the instruction in a easy tutorial.
I got no errors in every steps.
However, when I go to see the  results I got this:




Do you know how help me to fix the problem, please?
Thanks in advance
Good night 
Salvatore


Il giorno 24 juil. 2017, alle ore 19:40, Salvatore Esposito <[hidden email]> ha scritto:

Hi Scott
I’m glad to hear your answer soon. 
Thanks for your suggestion, honestly I didn’t know about jbrowse and no one told me about it.
I’m alone to do it. I would love to have a genome browser for our specie of interest, so all my colleague can use it to do their research.
I will try Jbrowse soon and If i could contact you in any case I could appreciate a lot.
Thanks for your help 
Sal



Il giorno 24 juil. 2017, alle ore 18:12, Scott Cain <[hidden email]> ha scritto:

Hi Salvatore,

Before we go down this path, since you are setting up a new system, is there a reason you don't want to use JBrowse (http://jbrowse.org/)? It is also a GMOD project and is in most respects, the successor of GBrowse.  It is significantly easier to set up and in general, most users find it much more appealing.  It can do just about everything GBrowse can do and some other things as well.  The list of things that GBrowse can do and JBrowse can't is relatively short and probably not important for a new genome project.  

Scott


On Mon, Jul 24, 2017 at 10:00 AM, Salvatore Esposito <[hidden email]> wrote:
Good morning all,
i'm an italian phD student working on wild potato. He have been sequenced the genome of our specie of interest and i'm now working on develop a genome browser dedicate on it.
I'm new user og GBrowse and I followed all the step required for the installation and setup.
I load also my file in correct folder:

- I created the folder cmm in  /var/lib/gbrowse2/databases
- I copied our annotation file inside named /var/lib/gbrowse2/databases/cmm/filtered_final_ok.gff

- after that i copied the cmm.conf in the folder /etc/gbrowse2
- and I manage also the /etc/gbrowse2/GBrowse.conf, adding the following line:


 [cmm]
description  = Tutorial database
path         = cmm.conf



So, everything should be fine, however I got this error when I try to connect to the server http://localhost/cgi-bin/gb2/gbrowse/cmm/ :


Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator at webmaster@localhost to inform them of the time this error occurred, and the actions you performed just before this error.

More information about this error may be available in the server error log.


Apache/2.4.10 (Ubuntu) Server at localhost Port 80


Could you help me to fix this problem and use the program?
Thanks in advance for your help
Sal


--
Salvatore Esposito, PhD Student
University of Naples "Federico II"
Department of Agricultural Sciences - Division of Plant genetics and biotechnology
Via Università, 100 - 80055 Portici (Italy)

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

-- 
Salvatore Esposito, PhD Student
University of Naples "Federico II"
Department of Agricultural Sciences
Via Università, 100 - 80055 Portici (Italy)




-- 
Salvatore Esposito, PhD Student
University of Naples "Federico II"
Department of Agricultural Sciences
Via Università, 100 - 80055 Portici (Italy)






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-gbrowse] GBrpwse2.0 error

Colin
The "Congratulations, jbrowse is on the web" + having a big red box with error normally scares people but it is actually normal if your data wasn't loaded yet



You can just continue to load your genome using prepare-refseqs.pl


-Colin

On Fri, Jul 28, 2017 at 10:06 AM, Scott Cain <[hidden email]> wrote:
Hi Sal,

I'm cc'ing the JBrowse mailing list so this conversation can be archived and others can chime in to help.  

When you say you followed all the tutorials, what does that mean exactly?  Did you run prepare-refseqs.pl and flatfile-to-json.pl? There is a reasonably good tutorial that I present in a few different settings, like this one that I gave at the Plant and Animal Genomes meeting in January: 


You wouldn't need the 3 GB virtualbox image linked at the top of the page, but you could use the commented out "curl" command in the "Setting up JBrowse" section to get the files used for the tutorial.

Scott


On Thu, Jul 27, 2017 at 5:47 PM, Salvatore Esposito <[hidden email]> wrote:
Hi Scott
how are you?
First, I wanna say you thanks again to suggest me jbrowse. I installed it and follow all the instruction in a easy tutorial.
I got no errors in every steps.
However, when I go to see the  results I got this:




Do you know how help me to fix the problem, please?
Thanks in advance
Good night 
Salvatore


Il giorno 24 juil. 2017, alle ore 19:40, Salvatore Esposito <[hidden email]> ha scritto:

Hi Scott
I’m glad to hear your answer soon. 
Thanks for your suggestion, honestly I didn’t know about jbrowse and no one told me about it.
I’m alone to do it. I would love to have a genome browser for our specie of interest, so all my colleague can use it to do their research.
I will try Jbrowse soon and If i could contact you in any case I could appreciate a lot.
Thanks for your help 
Sal



Il giorno 24 juil. 2017, alle ore 18:12, Scott Cain <[hidden email]> ha scritto:

Hi Salvatore,

Before we go down this path, since you are setting up a new system, is there a reason you don't want to use JBrowse (http://jbrowse.org/)? It is also a GMOD project and is in most respects, the successor of GBrowse.  It is significantly easier to set up and in general, most users find it much more appealing.  It can do just about everything GBrowse can do and some other things as well.  The list of things that GBrowse can do and JBrowse can't is relatively short and probably not important for a new genome project.  

Scott


On Mon, Jul 24, 2017 at 10:00 AM, Salvatore Esposito <[hidden email]> wrote:
Good morning all,
i'm an italian phD student working on wild potato. He have been sequenced the genome of our specie of interest and i'm now working on develop a genome browser dedicate on it.
I'm new user og GBrowse and I followed all the step required for the installation and setup.
I load also my file in correct folder:

- I created the folder cmm in  /var/lib/gbrowse2/databases
- I copied our annotation file inside named /var/lib/gbrowse2/databases/cmm/filtered_final_ok.gff

- after that i copied the cmm.conf in the folder /etc/gbrowse2
- and I manage also the /etc/gbrowse2/GBrowse.conf, adding the following line:


 [cmm]
description  = Tutorial database
path         = cmm.conf



So, everything should be fine, however I got this error when I try to connect to the server http://localhost/cgi-bin/gb2/gbrowse/cmm/ :


Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator at webmaster@localhost to inform them of the time this error occurred, and the actions you performed just before this error.

More information about this error may be available in the server error log.


Apache/2.4.10 (Ubuntu) Server at localhost Port 80


Could you help me to fix this problem and use the program?
Thanks in advance for your help
Sal


--
Salvatore Esposito, PhD Student
University of Naples "Federico II"
Department of Agricultural Sciences - Division of Plant genetics and biotechnology
Via Università, 100 - 80055 Portici (Italy)

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

-- 
Salvatore Esposito, PhD Student
University of Naples "Federico II"
Department of Agricultural Sciences
Via Università, 100 - 80055 Portici (Italy)




-- 
Salvatore Esposito, PhD Student
University of Naples "Federico II"
Department of Agricultural Sciences
Via Università, 100 - 80055 Portici (Italy)






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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